Hi Dan and thanks for the ideas!
Will it be possible to load cog-matrix calculated by cpp-traj directly
to the NetworkView in vmd avoiding using of CARMA? BTW is it possible
to convert parm7 to the pdf using some amber-tool?
Thanks,
James
2015-04-14 17:59 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> You can calculate various types of matrices with cpptraj ('matrix'
> command). You can also diagonalize the matrix and optionally write out
> nmwiz-compatible output ('diagmatrix' command). Cpptraj can use PSF
> and DCD files as well. See the Amber 14 manual for more details.
>
> -Dan
>
> On Tue, Apr 14, 2015 at 8:25 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>> Dear Amber users!
>>
>> I wonder to ask whether someone used VMDs NetworkView plugin for the
>> analysis of the biosimulations carried out in Amber? From the tutorial
>> I've found that to calculate covariance matrix prior to Networks
>> calculations some external programs like CARMA are used which directly
>> works with the NAMD-like psf topologies. Are there any other
>> possibilities to do the same using amber-like inputs?
>>
>>
>> Thanks!
>>
>> James
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Tue Apr 14 2015 - 12:00:03 PDT
